A new dihydroisocoumarins, 6-methoxy-8-hydroxy-3-(4-hydroxyphenyl) isochroman-1-one, named as hongkongenin (1), and seven known flavonoids were isolated from the methanol extract whole plant of Polygala hongkongensis Hemsl. Their structures were established on the basis of UV, IR, NMR, and MS spectral data. It is the first report of the occurrence of isocoumarins in Polygala, and the known compounds 2-8 were isolated from this plant for the first time. Flavonoids showed potent antioxidant activities in vitro against 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals, hydroxyl radicals, and reductive activity to Fe3+.